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### 3.2 QTL Projection

#### 3.2.1 Method

QTL projection consists in positioning the QTL located on a given map (the original map) onto another one (the reference map). To illustrate the basic principle of QTL projection, let's assume that the flanking markers of a given QTL location in the original map are also included in the reference. Then the QTL can be projected into the flanking marker interval of the reference map by using a simple homothetic rule. If the QTL have a confidence interval (CI) defined on the orignal map then it is resized on the reference map according to a scaling factor which takes into account the marker interval distance variations between the original and the reference map. This factor is computed by summing, over all the common marker sequences, the ratio of the marker interval distances between the reference and the original map weighted by the probability that the QTL lies in these intervals.

#### 3.2.2 QTLProj

QTLProj implements a dynamic algorithm in order to find the optimal context to do the projection. An optimal context consists in a pair of common marker which flanks the QTL in the original map and for which the distance estimate is consistent between the maps. Two parameters control the behaviour of the algorithm to find such a configuration: the minimal value of the ratio of the flanking marker interval distances and the minimal p-value obtained by testing the homogeneity of the flanking marker interval distances between the original and the reference map.

##### 3.2.2.1 Command Line Options

Option | Usage | Type | Explanation
--- | --- | --- | ---
`-m,--map` | required | string | The reference map (XML format).
`-q,--qtl` | required | string | The directory containing the original maps (XML format).
`-o,--output` | required | string | The output file stem.
`-r,--ratio` | optional | double | The minimal ratio between 0 and 1 (default is 0.5)
`-p,--pval` | optional | double | The minimal p-value between 0 and 1 (default is 0.01).
`--rmrk` | optional | string | A list of marker to ignore during the projection
`--rqtl` | optional | string | A list of QTL to be excluded from the projection

For example,

         %java org.metaqtl.main.QTLProj \
         >     -m reference.xml -q xmldb -o projection -r 0.25 -p 0.05

projects the QTL located onto the maps included in the directory `xmldb` on the reference map `reference.xml`. Only the QTL for which it is possible to find a pair of flanking markers for which the interval distance is not reduced by more than a factor of 0.25 or for which the p-value of the homogeneity test of equal distances is greater than 0.05 will be projected. If the `-v` option is activated, the programs will return as many WARNING outputs as the number of QTL for which the projection is not possible.

##### 3.2.2.2 Output files

QTLProj output consists in two XML files:

- `<output_stem>_map.xml` : This file contains both the markers and the projected QTL locations on the reference map (plus eventually the QTL previously defined on the reference).
- `<output_stem>_qtl.xml` : This file contains only the QTL which have been projected on the reference map (plus eventually the QTL previously defined on the reference).